Package ubic.gemma.cli.util

Class EntityLocatorImpl

java.lang.Object
ubic.gemma.cli.util.EntityLocatorImpl
All Implemented Interfaces:
EntityLocator
@Component public class EntityLocatorImpl extends Object implements EntityLocator

  • Constructor Summary

    Constructors
    Constructor
    Description
    EntityLocatorImpl()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    ubic.gemma.model.expression.arrayDesign.ArrayDesign
    locateArrayDesign(String identifier)
     
    ubic.gemma.model.expression.bioAssay.BioAssay
    locateBioAssay(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String sampleId)
     
    ubic.gemma.model.expression.bioAssay.BioAssay
    locateBioAssay(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String sampleId)
     
    ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics
    locateCellLevelCharacteristics(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String clcIdentifier)
     
    ubic.gemma.model.expression.bioAssayData.CellTypeAssignment
    locateCellTypeAssignment(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String cta)
     
    ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
    locateDiffExAnalysis(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String analysisIdentifier)
     
    ubic.gemma.model.expression.experiment.ExperimentalFactor
    locateExperimentalFactor(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, String identifier)
     
    ubic.gemma.model.expression.experiment.ExpressionExperiment
    locateExpressionExperiment(String identifier, boolean useReferencesIfPossible)
    Attempt to locate an experiment using the given identifier.
    ubic.gemma.model.common.protocol.Protocol
    locateProtocol(String protocolName)
     
    <T extends ubic.gemma.model.expression.bioAssayData.DataVector>
    ubic.gemma.model.common.quantitationtype.QuantitationType
    locateQuantitationType(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String qt, Class<? extends T> vectorType)
     
    <T extends ubic.gemma.model.expression.bioAssayData.DataVector>
    org.apache.commons.lang3.tuple.Pair<Class<? extends T>,ubic.gemma.model.common.quantitationtype.QuantitationType>
    locateQuantitationType(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorTypes)
     
    ubic.gemma.model.genome.Taxon
    locateTaxon(String identifier)
     

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • EntityLocatorImpl

      public EntityLocatorImpl()

  • Method Details

    • locateTaxon

      public ubic.gemma.model.genome.Taxon locateTaxon(String identifier)
      Specified by:
      locateTaxon in interface EntityLocator

    • locateArrayDesign

      public ubic.gemma.model.expression.arrayDesign.ArrayDesign locateArrayDesign(String identifier)
      Specified by:
      locateArrayDesign in interface EntityLocator

    • locateExpressionExperiment

      public ubic.gemma.model.expression.experiment.ExpressionExperiment locateExpressionExperiment(String identifier, boolean useReferencesIfPossible)
      Attempt to locate an experiment using the given identifier.
      Specified by:
      locateExpressionExperiment in interface EntityLocator

    • locateProtocol

      public ubic.gemma.model.common.protocol.Protocol locateProtocol(String protocolName)
      Specified by:
      locateProtocol in interface EntityLocator

    • locateQuantitationType

      public <T extends ubic.gemma.model.expression.bioAssayData.DataVector> ubic.gemma.model.common.quantitationtype.QuantitationType locateQuantitationType(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String qt, Class<? extends T> vectorType)
      Specified by:
      locateQuantitationType in interface EntityLocator

    • locateQuantitationType

      public <T extends ubic.gemma.model.expression.bioAssayData.DataVector> org.apache.commons.lang3.tuple.Pair<Class<? extends T>,ubic.gemma.model.common.quantitationtype.QuantitationType> locateQuantitationType(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorTypes)
      Specified by:
      locateQuantitationType in interface EntityLocator

    • locateCellTypeAssignment

      public ubic.gemma.model.expression.bioAssayData.CellTypeAssignment locateCellTypeAssignment(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String cta)
      Specified by:
      locateCellTypeAssignment in interface EntityLocator

    • locateCellLevelCharacteristics

      public ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics locateCellLevelCharacteristics(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String clcIdentifier)
      Specified by:
      locateCellLevelCharacteristics in interface EntityLocator

    • locateExperimentalFactor

      public ubic.gemma.model.expression.experiment.ExperimentalFactor locateExperimentalFactor(ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment, String identifier)
      Specified by:
      locateExperimentalFactor in interface EntityLocator

    • locateBioAssay

      public ubic.gemma.model.expression.bioAssay.BioAssay locateBioAssay(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String sampleId)
      Specified by:
      locateBioAssay in interface EntityLocator

    • locateBioAssay

      public ubic.gemma.model.expression.bioAssay.BioAssay locateBioAssay(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, String sampleId)
      Specified by:
      locateBioAssay in interface EntityLocator

    • locateDiffExAnalysis

      public ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis locateDiffExAnalysis(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, String analysisIdentifier)
      Specified by:
      locateDiffExAnalysis in interface EntityLocator